Alignments for a candidate for ilvD in Desulfovibrio bastinii DSM 16055

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfovibrio bastinii DSM 16055

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_034632534.1 G496_RS0105830 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-11919
         (549 letters)



>NCBI__GCF_000429985.1:WP_034632534.1
          Length = 573

 Score =  372 bits (954), Expect = e-107
 Identities = 229/563 (40%), Positives = 321/563 (57%), Gaps = 39/563 (6%)

Query: 17  SLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEGVNAAGGVAFEFNTMAI 76
           +L+     T DD EKP I + + + D  PG  HL  L+     G+  AGG   +F+   I
Sbjct: 18  ALMMGMNWTRDDVEKPQILVDDVHGDSHPGSYHLDVLSNEASTGIYEAGGRPAQFHVTDI 77

Query: 77  CDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPGMLMAAARLDIP 136
           CDG A  H+GM + L SR I+AD VE  A     DG++LL  CDK  P  LMAAAR+DIP
Sbjct: 78  CDGWAQGHEGMNFILCSRGIIADMVEIHASVIPWDGMILLSGCDKSTPAHLMAAARMDIP 137

Query: 137 AIVVTGGPML--PGEFKGRKVDLINVYEGVGTVSAGEMSEDELEELERCACPGPRSCAGL 194
            I + GG M   PG         ++  +  G V   EM + +L       CP   +C  +
Sbjct: 138 TIHIPGGAMRSGPGNSTSGLAGPLSARKKKGLVEPAEMRDYKL-----TGCPSCGACQFM 192

Query: 195 FTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQENLKPTMIMSQEAF 254
            TA+TM C++EALGM+LPG A   A  +  +++AR +GK+I+ + ++ +    I+++  F
Sbjct: 193 GTASTMQCMSEALGMALPGTALMPATMNDIKRMARAAGKQIMYLAEKGITARKILTKANF 252

Query: 255 ENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHIASISPAGEHMMLD 314
            NA+ V  A+GGSTN  +H+PAIA E+ G+ I+   FD + + I ++ ++ P+G++    
Sbjct: 253 MNAMKVHAAIGGSTNAYIHMPAIAHEL-GIKIDPKEFDAIGQEIKYLTNVQPSGKYTAEL 311

Query: 315 LDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIE----------------NVKVGHRDV 358
              AGGIP V   L D ++ + +T TGRT+ +++E                +  +   ++
Sbjct: 312 FWFAGGIPMVQHMLRDQLDLDVMTVTGRTLGDSLEILEQDGFFNRCHGHLKSYNIPRNEI 371

Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418
           IR  +    S G +A+L GN+AP+GSVVK  AV  DM  H GPA VFNSED+   AI  G
Sbjct: 372 IRTTEESTKS-GSIAVLDGNIAPKGSVVKYAAVKPDMHKHVGPAAVFNSEDDAQAAIIAG 430

Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIA--GMGLERVALITDGRFSGGTRGPCVGH 476
           +I+ G V+VIRYEGPKG  GM EM   T AI         VAL+TDGRFSG T GPC+GH
Sbjct: 431 QINPGSVVVIRYEGPKGS-GMPEMFMTTDAIVYDEKLNGTVALVTDGRFSGATSGPCIGH 489

Query: 477 VSPEAMEDGPLAAVNDGDIIRIDIPSRKLEV------DLSPREIE----ERLQSAVKPRR 526
           VSPEA++ GP+A + D DII IDIPSR L+V      + +P+E+E    ER ++   P R
Sbjct: 490 VSPEAVDGGPIALLEDDDIISIDIPSRSLQVIGVKGEEKTPKEMEAILAERRKNWTLPER 549

Query: 527 -SVKGWLARYRKLAGSADTGAVL 548
              KG L RY   A SA  GA +
Sbjct: 550 PQKKGVLKRYSDSAVSAMEGAYM 572


Lambda     K      H
   0.319    0.136    0.397 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 896
Number of extensions: 56
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 549
Length of database: 573
Length adjustment: 36
Effective length of query: 513
Effective length of database: 537
Effective search space:   275481
Effective search space used:   275481
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis